diff --git a/api/core/mcp/session/base_session.py b/api/core/mcp/session/base_session.py
index 1c0f582501..dd2ab25527 100644
--- a/api/core/mcp/session/base_session.py
+++ b/api/core/mcp/session/base_session.py
@@ -171,6 +171,9 @@ class BaseSession(
         self._session_read_timeout_seconds = read_timeout_seconds
         self._in_flight = {}
         self._exit_stack = ExitStack()
+        # Initialize executor and future to None for proper cleanup checks
+        self._executor = None
+        self._receiver_future = None
 
     def __enter__(self) -> Self:
         self._executor = ThreadPoolExecutor()
@@ -184,10 +187,21 @@ class BaseSession(
     def __exit__(
         self, exc_type: type[BaseException] | None, exc_val: BaseException | None, exc_tb: TracebackType | None
     ) -> None:
-        self._exit_stack.close()
         self._read_stream.put(None)
         self._write_stream.put(None)
 
+        # Wait for the receiver loop to finish
+        if self._receiver_future:
+            try:
+                self._receiver_future.result(timeout=5.0)  # Wait up to 5 seconds
+            except Exception:
+                # If the receiver loop is still running after timeout, we'll force shutdown
+                pass
+
+        # Shutdown the executor
+        if self._executor:
+            self._executor.shutdown(wait=True, timeout=5.0)
+
     def send_request(
         self,
         request: SendRequestT,